Engineering bacteria to make petroleum substitute, pump out hydrocarbons.

Bacteria are big news in the biofuel business—genetically engineered microorganisms can turn various combinations of biomass, sunlight, and even carbon dioxide into liquid fuels. The potential for replacing fossil fuels with these renewable energy sources is significant, but the efficient implementation of these technologies remains complicated.

Two studies published in the Proceedings of the National Academy of Sciences this week looked at how to make biofuel production more efficient.

A team of British scientists genetically engineered E. coli bacteria to produce a hydrocarbon molecule that mimics petroleum. Right now, conventional biofuels like ethanol have to be blended with sufficient traditional fuel so that our engines don’t detect their presence. These "mimic molecules," on the other hand, could go straight into our existing engines.

Many hurdles remain to scaling up these engineered bacteria, but the researchers believe it could be a viable alternative to producing ethanol from food crops.

To harvest the fuel molecules produced by a microorganism like E. coli or algae typically requires killing the cell, but new research shows that existing cellular transport mechanisms can be harnessed to excrete biofuel molecules so that cells can continue production over time. “It’s the same idea as milking a cow,” said Geoffrey Chang, a professor of pharmacy at the University of California San Diego.

What brought a pharmacist into biofuel research? Drugs and biofuels are both greasy molecules, so Chang and his colleagues decided to see if they could apply what they knew about the systems that transport pharmaceutical molecules through cell membranes.

Chang and his co-authors, Rupak Doshi and Tuan Nguyen, created a model system using E. coli bacteria that produced molecules called carotenoids. Carotenoids have a similar structure to several biofuel molecules, but they are colorful enough that the researchers could see the transportation in action.

They focused on a common family of transport proteins known as the ATP binding cassette transporters (typically called the ABC transporters), which excrete a variety of greasy molecules, like lipids and steroids.

“The idea is that you can plug and play this transport system. These are ABC transporters, so many organisms have them already,” Chang said.

For many of the microorganisms that have been engineered to produce valuable biofuels, the fuel molecules are toxic. If the cells can pump out the molecules, they can continue to make more without killing themselves.

The E. coli used in the experiment could continue to produce and secrete carotenoids for days. It’s only a model, but because the ABC transporters are common and relatively promiscuous, the approach could be applied in a wide variety of systems. In a practical application, an algae-based system could theoretically continually produce and secrete biofuels indefinitely.

Chang believes that these secretion systems could be a game changer that makes production of biofuels more cost effective. He’s not alone—the leading consumer of jet fuel, the US Air Force, funded the research.

This could be great if all of the carbon used in the synthetic fuels was taken from the atmosphere. Fuel production and use would become closed loop. Or just take the algae-produce petroleum and pump it right back down in the ground.

This could be great if all of the carbon used in the synthetic fuels was taken from the atmosphere. Fuel production and use would become closed loop. Or just take the algae-produce petroleum and pump it right back down in the ground.

I've entertained the notion of writing a futuristic sci-fi, where the petro-algae are scrubing so much CO2 from the atmosphere, global cooling is the problem.

The article picture, Its not a "growing chamber" for algae. Its a PhotoBioReactor, or PBR for short, in which algae grows.

This is not a new concept, using E-coli, its been around for years, and neither is using algae a new concept as its been around for years also as has the concept of using the oil from algae then processing it into fuel.

Great. So folks can continue the use of hydrocarbon fuels with reduced incentive to invest in or explore cleaner alternatives.

If you're pulling the carbon out of the atmosphere to do so, what exactly is the problem?

Pretty sure adding greenhouse gases to the atmo is not the only issue with burning hydrocarbons.

Having said that, this certainly seems like a superior option to finding, digging up, and processing liquefied dead dinosaurs. One step closer to making the best use of the largest fusion reactor we have access to (in that the algae are solar-powered) .

The key disruption here is releasing oil from the cell without destroying it — that's new. But using this new method will require a new technique for separating the oil product from the algae slurry.

If the crop is destroyed anyway, separating is relatively easy; pull off the oil, dry out the biomass, and you get oil, cellulose, and water. If your process is solvent-free, all three products are safe to be used in other processes. But if you have to keep the crop alive, now you have to revisit the separation problem again, because current methods of separating oil from slurry would involve materials or temperatures hazardous to algae.

It may be that it's cheaper to use a solvent-free lysing process that destroys the cells but simplifies separation than it would be to try to separate from a living slurry and still keep it alive.

In any case, this sets a new bar for algae biofuels: release the oil while preserving the crop and avoiding toxic materials.

The key disruption here is releasing oil from the cell without destroying it — that's new. But using this new method will require a new technique for separating the oil product from the algae slurry.

If the crop is destroyed anyway, separating is relatively easy; pull off the oil, dry out the biomass, and you get oil, cellulose, and water. If your process is solvent-free, all three products are safe to be used in their processes. But if you have to keep the crop alive, now you have to revisit the separation problem again, because current methods of separating oil from slurry would involve materials or temperatures hazardous to algae.

It may be that it's cheaper to use a solvent-free lysing process that destroys the cells but simplifies separation than it would be to try to separate from a living slurry and still keep it alive.

In any case, this sets a new bar for algae biofuels: release the oil while preserving the crop and avoiding toxic materials.

Assuming you are right, this is going to come out sounding some kind of combination of sarcastic or ignorant, so I apologize: Doesn't oil float?

The key disruption here is releasing oil from the cell without destroying it — that's new. But using this new method will require a new technique for separating the oil product from the algae slurry.

If the crop is destroyed anyway, separating is relatively easy; pull off the oil, dry out the biomass, and you get oil, cellulose, and water. If your process is solvent-free, all three products are safe to be used in their processes. But if you have to keep the crop alive, now you have to revisit the separation problem again, because current methods of separating oil from slurry would involve materials or temperatures hazardous to algae.

It may be that it's cheaper to use a solvent-free lysing process that destroys the cells but simplifies separation than it would be to try to separate from a living slurry and still keep it alive.

In any case, this sets a new bar for algae biofuels: release the oil while preserving the crop and avoiding toxic materials.

Here's the deal with algae, you can not release enough oil without destroying the algae cell. The majority of oil in algae is still held in the cell (almost 80%) even with this method. This means a new crop of algae for each crop of oil. The method they are using here is not really new, its been tried before and it doesn't work in the prolonged continuous batch mode needed to produce a worthwhile batch of oil on a continuous basis. Exxon tried it, various other algae companies tried it. I guess they could improve upon it in some way, but one of the algae companys that was funded by the Navy a few years ago for algae based fuels failed to produce enough oil using this method so had to switch to an electrical cell disruption method. So maybe the have something improved here, time will tell.

The key disruption here is releasing oil from the cell without destroying it — that's new. But using this new method will require a new technique for separating the oil product from the algae slurry.

If the crop is destroyed anyway, separating is relatively easy; pull off the oil, dry out the biomass, and you get oil, cellulose, and water. If your process is solvent-free, all three products are safe to be used in their processes. But if you have to keep the crop alive, now you have to revisit the separation problem again, because current methods of separating oil from slurry would involve materials or temperatures hazardous to algae.

It may be that it's cheaper to use a solvent-free lysing process that destroys the cells but simplifies separation than it would be to try to separate from a living slurry and still keep it alive.

In any case, this sets a new bar for algae biofuels: release the oil while preserving the crop and avoiding toxic materials.

Assuming you are right, this is going to come out sounding some kind of combination of sarcastic or ignorant, so I apologize: Doesn't oil float?

And, further, isn't oil more volatile than water? I, in my relative ignorance, would think that they could let it evaporate then condense it in a collector.

Great. So folks can continue the use of hydrocarbon fuels with reduced incentive to invest in or explore cleaner alternatives.

If you're pulling the carbon out of the atmosphere to do so, what exactly is the problem?

Pretty sure adding greenhouse gases to the atmo is not the only issue with burning hydrocarbons.

Having said that, this certainly seems like a superior option to finding, digging up, and processing liquefied dead dinosaurs. One step closer to making the best use of the largest fusion reactor we have access to (in that the algae are solar-powered) .

The next step would be fuel cells, which would eliminate the NO2. Then you'd really end up with just H2O+CO2 at the tailpipe.

The key disruption here is releasing oil from the cell without destroying it — that's new. But using this new method will require a new technique for separating the oil product from the algae slurry.

If the crop is destroyed anyway, separating is relatively easy; pull off the oil, dry out the biomass, and you get oil, cellulose, and water. If your process is solvent-free, all three products are safe to be used in their processes. But if you have to keep the crop alive, now you have to revisit the separation problem again, because current methods of separating oil from slurry would involve materials or temperatures hazardous to algae.

It may be that it's cheaper to use a solvent-free lysing process that destroys the cells but simplifies separation than it would be to try to separate from a living slurry and still keep it alive.

In any case, this sets a new bar for algae biofuels: release the oil while preserving the crop and avoiding toxic materials.

Assuming you are right, this is going to come out sounding some kind of combination of sarcastic or ignorant, so I apologize: Doesn't oil float?

In clear water, yes, but the oil+water+algae slurry is more of an emulsion, and you're dealing with a tiny, tiny volume of oil relative to the biomass and water, so it won't exactly form a visible layer.

Typical separation methods involve things like membranes, osmosis, and distillation, which algae wouldn't necessarily survive in any useful way. And in the case of active methods, they require considerable energy. That's why I'm thinking the next problem is to commercialize an end-to-end process that makes it cheaper to treat with E.coli and keep the crop than to discard the crop and sell the biomass byproduct.

Sounds like a pretty cool start. I'd be interested to know more about what can be used to supply the algae. Punchline aside, could we turn sewage treatment plants into fuel producers? How precise is the engineering required; could we tailor the output to produce ideal fuels? Different types of fuel (gasoline, diesel, fuel oil, etc)?

How demanding (both safety and general resources) is the bioreactor? Could you have what amount to gasoline-producing septic systems?

If it's related to drugs, imagine having to try and ignore the fact that the ibuprofen you're about to take may have been last week's meatloaf.

Still, if the E.coli lives long enough to produce and excrete a sufficient amount of oil, then killing it isn't the hurdle it might otherwise seem. If it can produce indefinitely, isn't there a point where simply leaving it in and just pulling the water out would still leave a fuel good enough to use? Or maybe just that at some set point enough fuel is created that the batch can be harvested, and a new batch started and still have it be economically feasible.

I could also see that this might (with a ton of refinement of the process) allow more self sufficiency for countries all over the world, as it may not be as location specific as solar or wind.

Here's the deal with algae, you can not release enough oil without destroying the algae cell. The majority of oil in algae is still held in the cell (almost 80%) even with this method. This means a new crop of algae for each crop of oil. The method they are using here is not really new, its been tried before and it doesn't work in the prolonged continuous batch mode needed to produce a worthwhile batch of oil on a continuous basis. Exxon tried it, various other algae companies tried it.

While the method has been tried before, this demonstrates some progress in oil yield. The technique isn't a total dead-end. All you have to do is improve the yield enough to make keeping the crop more cost-effective than destroying it. The work on E.coli should probably continue. But yes, the fullest oil yield is going to involve destroying the cell.

In clear water, yes, but the oil+water+algae slurry is more of an emulsion, and you're dealing with a tiny, tiny volume of oil relative to the biomass and water, so it won't exactly form a visible layer.

Typical separation methods involve things like membranes, osmosis, and distillation, which algae wouldn't necessarily survive in any useful way. And in the case of active methods, they require considerable energy. That's why I'm thinking the next problem is to commercialize an end-to-end process that makes it cheaper to treat with E.coli and keep the crop than to discard the crop and sell the biomass byproduct.

Allow me to continue with my partial understanding, then:

Aren't typical separation methods designed around the fact that the oil is in the algae, not the water? At least until the algae are crushed/destroyed somehow? It seems like that would limit the concentration of oil in a way that this system would not, since the algae can only sustain so much oil inside before it's time to harvest. Under this system, it seems like you could end up with a much higher concentration of oil in the water. Enough for a microbe-survivable spin in a centrifuge for separation, maybe?

(I'm not questioning your knowledge, just trying to understand.)

EDIT: I think someone else just answered the question. Still way too much oil stays in the algae, so it's not really working the way I was imagining.

Great. So folks can continue the use of hydrocarbon fuels with reduced incentive to invest in or explore cleaner alternatives.

You do get that the ENTIRE WORLD is set up for this kind of fuel right? And that there is NOTHING even on the horizon that has enough REAL promise of replacing it? We use what we have until we find something that can realistically fill our needs and replace it.

Here's the deal with algae, you can not release enough oil without destroying the algae cell. The majority of oil in algae is still held in the cell (almost 80%) even with this method. This means a new crop of algae for each crop of oil. The method they are using here is not really new, its been tried before and it doesn't work in the prolonged continuous batch mode needed to produce a worthwhile batch of oil on a continuous basis. Exxon tried it, various other algae companies tried it.

While the method has been tried before, this demonstrates some progress in oil yield. The technique isn't a total dead-end. All you have to do is improve the yield enough to make keeping the crop more cost-effective than destroying it. The work on E.coli should probably continue. But yes, the fullest oil yield is going to involve destroying the cell.

This could be great if all of the carbon used in the synthetic fuels was taken from the atmosphere. Fuel production and use would become closed loop. Or just take the algae-produce petroleum and pump it right back down in the ground.

I've entertained the notion of writing a futuristic sci-fi, where the petro-algae are scrubing so much CO2 from the atmosphere, global cooling is the problem.

Here's the deal with algae, you can not release enough oil without destroying the algae cell. The majority of oil in algae is still held in the cell (almost 80%) even with this method. This means a new crop of algae for each crop of oil. The method they are using here is not really new, its been tried before and it doesn't work in the prolonged continuous batch mode needed to produce a worthwhile batch of oil on a continuous basis. Exxon tried it, various other algae companies tried it. I guess they could improve upon it in some way, but one of the algae companys that was funded by the Navy a few years ago for algae based fuels failed to produce enough oil using this method so had to switch to an electrical cell disruption method. So maybe the have something improved here, time will tell.

Disclaimer: I am not in any way officially qualified to judge the merits of this discussion

With that stated, I gathered that the E. coli was essentially pumping out hydrocarbons from waste cellulose feed stock. If that is the case, and I have not failed reading comprehension, then couldn't the algae be modified with this method to also secrete fuel molecules? If not, then when the algae is full, for lack of a better term, run it through the presses and use the remainder as feed stock for the E. coli. The remaining oil/fuel could be ported out by the bacteria, vastly increasing the current yield, plus converting what is left. Am I missing something here?

I'd be interested to know more about what can be used to supply the algae. Punchline aside, could we turn sewage treatment plants into fuel producers?

To varying degrees, depending on the process. Sewage adds hazards that aren't terribly cost-effective to manage, although work has been done on this. Farmland ponds and things like that, though, are usable today at low to moderate yield.

As an aside, the fuel story is exciting, but that's only one part commercial algae processing. Algae is used for lots of things, and much of the work goes into making as many of its products as useful as possible, of which separating usable oil is just one part.

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How precise is the engineering required; could we tailor the output to produce ideal fuels? Different types of fuel (gasoline, diesel, fuel oil, etc)?

As with any oil, it's got to be refined first. What you mostly get from algae oil is in the area of bunker fuel, Jet-A, and diesel.

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How demanding (both safety and general resources) is the bioreactor? Could you have what amount to gasoline-producing septic systems?

In general, they only get complicated when an algae systems vendor has something to sell. But I don't exactly think you'll see E.coli Septic Bio-Gojuice™ kits at Tractor Supply any time soon. Nobody really wants to deal with bacteria at commercial scale, except the pharmaceutical companies.

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If it's related to drugs, imagine having to try and ignore the fact that the ibuprofen you're about to take may have been last week's meatloaf.

Yeah… there's much worse than that in any given pharmaceutical product. Enjoy!

This sounds a bit more refined (I understand that e.coli is considered easy to work with), but I recall a similar plan a few years ago for diatoms. The plan was to hijack their process for secreating their shells and use that to secrete the fuel instead.

And for the people who want off of oil completely, there's still value in plastics, even if we all have electric cars.

What are the odds that getting this process to work in E. coli is just a proof of concept, and the whole set of genes could eventually be transferred to another organism: a microbe that sticks to the walls, so you can run the food/excretions past them, or even an animal that actually can be "milked?" Is there a good reason why this couldn't happen?

Here's the deal with algae, you can not release enough oil without destroying the algae cell. The majority of oil in algae is still held in the cell (almost 80%) even with this method. This means a new crop of algae for each crop of oil. The method they are using here is not really new, its been tried before and it doesn't work in the prolonged continuous batch mode needed to produce a worthwhile batch of oil on a continuous basis. Exxon tried it, various other algae companies tried it. I guess they could improve upon it in some way, but one of the algae companys that was funded by the Navy a few years ago for algae based fuels failed to produce enough oil using this method so had to switch to an electrical cell disruption method. So maybe the have something improved here, time will tell.

Disclaimer: I am not in any way officially qualified to judge the merits of this discussion

With that stated, I gathered that the E. coli was essentially pumping out hydrocarbons from waste cellulose feed stock. If that is the case, and I have not failed reading comprehension, then couldn't the algae be modified with this method to also secrete fuel molecules? If not, then when the algae is full, for lack of a better term, run it through the presses and use the remainder as feed stock for the E. coli. The remaining oil/fuel could be ported out by the bacteria, vastly increasing the current yield, plus converting what is left. Am I missing something here?

I'm not an expert, but I have had some experience with producing fuel from algae commercially using e-coli and other methods. There is a lot to it, but i'll gloss over it some and its been a while. Its not as easy as it sounds, algae are amazingly resistant to change in their basic functions. All algae produce oil, some more than others. Photosynthetic algae use sunlight + water + carbon dioxide, manufacturing sugars and releasing oxygen as a waste by-product. Algae breaks down the larger sugar molecules two carbons at a time and makes fatty acids. When the algae is happy the fatty acids are used for new cell membrane or to make other algae cells. Algae are also gluttons, they overeat most of the time and when they overeat or are under stress that limits their growth those fatty acids are converted to triglycerides by bonding three fatty acid molecules to a three carbon glycerol molecule and this ends up as a fat stored as oil. Its that oil that needs to be converted to fuel.

If they can convince the e-coli to produce fuel directly in the algae oil without killing the algae cell and still get a great enough harvest it would be great, but even then they would probably end up having to destroy the cell to get enough yield. Heterotrophic algae methods (known as 'Dark Fermentation' by some, oddly enough its production is very similar to that used to brew beer) is basically the same, except they need sugars added as the algae energy source instead of sunlight, but there are no naturally occurring heterotrophic algae which produce suitable amounts of oil worth it without genetic engineering methods applied which raises cost for the heterotrophic methods plus the heterotrophic method for the sugars would require feed crop type sources for large scale production which also increases cost. So Photosynthetic algae is the best bet. However, the more financially viable oil harvest will come from destroying the cell which mechanical presses don't do a very good job with, especially in a continuous batch mode process, so other methods such as an electrical cell disruption method will need to be applied which can be applied while the algae is still wet because while most algae is still wet is when its quicker to destroy the cell via cell disruption methods which can operate in a continuous batch mode process. Even if the e-coli can convert the oil to fuel in the algae the cell would still need to be destroyed to get the greatest harvest because that greater amount of converted fuel would still be contained in the cell, algae is funny that way, as a general rule of thumb the greater the oil producing capability of the algae the more the algae cell hangs onto in the cell, it holds onto what it has even in death so it would take destroying the cell to get to that greater amount of oil or fuel. Its possible to coax the algae into releasing a greater amount of oil from the cell than it would release naturally, so that would be something to look at for improvement in the e-coli method. Its pretty likely though in most cases of financially viable commercial production you would not be left with any viable biomass feed stock for the e-coli after the fact because the cell would be dead once destroyed and most if not all of its oil would have been released anyway so why not harvest it then instead of another step to add e-coli and besides there would be little for the e-coli to work on anyway at that point. No process will be viable for large scale use unless its financially viable. Right now, as it stands today, Photosynthetic algae produces oil which is more compatible with current refinery methods and closer to the fuels we use now in vehicles than heterotrophic method algae, and its cheaper without resorting to e-coli, however, if the e-coli process can be improved it would be great. Presumably the photobioreactor (PBR, and not a 'growth chamber' which the picture with the article does not show, its a PBR in the picture and there is a really big difference between the two the picture title is not correct and is 100% wrong) would be used because its more efficient, controllable, and predictable for parameters and yield. So maybe they will do something different with this re-interpretation of the e-coli method and you could turn out to be right with your idea.

Kate Prengaman / Kate is a science and environmental reporter living in Yakima, Washington. She writes about everything from emerging energy technology to persistent environmental problems and she really likes plants.